You suggestion of a mux could be done, but there are a lot of trade-offs. I do not work for Carloop, so the actual rationale may be a bit different than my thoughts.
To start, here in North America, the only legally required CANbus is the one that Carloop interfaces with. To implement only that bus means a simple device that is easy to build, small enough to fit in the package it does, and would meet the majority of use cases.
To add a second CANbus for the Photon, it means adding a mux, an additional CAN transceiver and all the circuitry to support that. That could likely double the physical size of the Carloop and it would no longer fit directly on the OBD2 port. That would also make it a lot more expensive. Then, there is the question of how many vehicle models have a second CANbus on that port; it would not be that many. For some models of cars, it would then be necessary to be able to disable the second CANbus at high impedance since the pins are used for other purposes that are not compatible, making things further complicated.
Once that hardware layer is in place, you could still only communicate with single CANbus at a time. That means that you have to miss out completely on what is happening on the CANbus that you are not connected to at that time. That might be seen as a big limitation.
Here is what is usually, but not always, available on the OBD2 port at this Wikipedia page:
As you can see, it gets hard to do a design that covers all the possibilities. You quickly getting into customizing things for a particular vehicle.
My opinion is that Carloop did a very good job of providing the right functionality for an almost-consumer level product.
Don't forget that the design is completely open-source, so it is possible to customize both the hardware and firmware to fit your particular use case.